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The largest part of the country lies between two rivers, the Dniester and the Prut. Moldova's rich soil and temperate continental climate (with warm summers and mild winters) have made the country one of the most productive agricultural regions since ancient times, and a major supplier of agricultural products in southeastern Europe. The western border of Moldova is formed by the Prut river, which joins the Danube before flowing into the Black Sea. In the north-east, the Dniester is the main river, flowing through the country from north to south, receiving the waters of Răut, Bâc, Ichel, Botna. Ialpug flows into one of the Danube limans, while Cogâlnic into the Black Sea chain of limans.

The country is landlocked, even though it is very close to the Black Sea. While the northern part of the country is hilly, elevations never exceed 430 meters (1,411 ft)—the highest point being the Bălăneşti Hill. Moldova's hills are part of the Moldavian Plateau, which geologically originate from the Carpathian Mountains. Its subdivisions in Moldova include Dniester Hills (Northern Moldavian Hills and Dniester-Rāut Ridge), Moldavian Plain (Middle Prut Valley and Bălţi Steppe), and Central Moldavian Plateau (Ciuluc-Soloneţ Hills, Corneşti Hills (Codri Massive) - Codri, meaning "forests" -, Lower Dniester Hills, Lower Prut Valley, and Tigheci Hills). In the south, the country has a small flatland, the Bugeac Plain. The territory of Moldova east of the river Dniester is split between parts of the Podolian Plateau, and parts of the Eurasian Steppe.

Phytogeographically, Moldova is shared between the Central European and Eastern European provinces of the Circumboreal Region within the Boreal Kingdom. According to the WWF, the territory of Moldova can be subdivided into three ecoregions: the Central European mixed forests, the East European forest steppe (the most territory of the country), and Pontic steppe (in the south and southeast).